Copy number variation (CNV) is a significant source of genomic diversity and human disease9,10. Subtelomeric CNVs are large deletions, duplications, and translocations that occur at chromosome ends and are responsible for 3-6% of idiopathic mental retardation cases6,11-13. Individuals with subtelomeric rearrangements have intellectual disabilities, autism, dysmorphic features, and/or other birth defects. Children are typically diagnosed with a subtelomeric rearrangement using cytogenetic tests such as subtelomeric fluorescence in situ hybridization (FISH) or array comparative genomic hybridization (CGH). Subtelomeric rearrangements have been estimated to account for up to 30% of pathogenic CNVs detected in affected children9,14, and the overall prevalence of subtelomeric rearrangements is estimated at 1/10,00015. Despite the impact on human health, very little is known about the mechanisms of chromosome breakage and repair that give rise to subtelomeric CNV. Research on the fundamental biology of CNV formation is critical to understanding the causes of and risk factors associated with disease-causing structural rearrangements. We hypothesize that particular DNA sequences are susceptible to breakage. To this end, we propose to isolate human DNA sequences that underlie subtelomeric breakage sites and functionally dissect the motifs that cause double-strand breaks (DSBs). The aims of this proposal are to 1) fine-map subtelomeric breakpoints, 2) identify subtelomeric sequence motifs that contribute to genomic instability, and 3) functionally annotate breakage motifs in a yeast gross chromosomal rearrangement (GCR) assay that quantifies chromosome breakage in the subtelomeric sequence. Integrated genomic, bioinformatics, and in vivo breakage experiments will determine whether or not DNA sequence plays a role in subtelomeric breakage. Our studies will also capture the genomic structure of subtelomeric rearrangements, which will allow us to determine the mechanisms of repair acting on subtelomeric DSBs. This proposal promises to reveal new sequence motifs that promote genomic instability and novel mechanisms of DNA repair. These data will be critical to understanding the forces that shape subtelomeric rearrangements and other CNV throughout the human genome.